Structural BioinformaticsIn parallel to a dramatic growth of the sequence databases (~350,000 entires in 1999) in the past decade, structural databases, which are still relatively small (~10,000 entries), also followed the same exponential growth. The total number of protein folds is currently estimated to be between 5,000 and 6,000; each protein has its own biological function yet often shares the same fold with other proteins. The EF-hand protein superfamily is a good example of this: all proteins in the superfamily contain the simple helix-loop-helix motif which is responsible for Ca2+ binding, yet perform diverse biological functions. It is therefore important to precisely characterise differences and similarities in structure between various proteins within the same family. We have developed a computational tool to characterize the conformational states and changes of EF-hand proteins (Yap et al., 1999), revealing a structural diversity of this large protein superfamily. More recently we have been developing structural databases for calmodulin binding proteins and cadherins
Yap, K.L., Ames, J.B., Swindells, M.B. and Ikura, M. (1999) Diversity of Conformational States and Changes within the EF-hand Protein Superfamily. Proteins 37, 499-507.
Yap, K.L., Ames, J.B., Swindells, M.B. and Ikura, M. (2002) Vector Geometry Mapping: A Method to Characterise the Conformation of Helix-Loop-Helix Calcium Binding Proteins. Methods Mol. Biol. 173:317-324.